Microbes clean our oceans

Oil spills are a major threat to the marine environment. The chemical components of crude oil can smother or poison marine organisms causing great harm. Whilst these spills are detrimental to the environment, further damage may also occur during the clean-up process due to the invasive nature of particular cleaning techniques. This paper looks at the clean-up operation for the Deepwater Horizon drilling rig spill of 2010 that was the biggest accidental release of crude oil recorded to date. The majority of the oil from this spill reaches the sandy benthic habitat that dominates this area where microbial biofilms are situated. These biofilms are capable of bioremediation, however there is a lack of information as to the exact microbes that are responsible for this oil degradation within the communities. This experiments aim was to expand on this knowledge and investigate the bioremediation response by characterising the community structure involved with oil degradation.

Sand samples were taken from the affected area for investigation, the microbes from which were grown using 2 methods. One of these was by traditional culturing techniques involving the use of an artificial seawater medium, both aerobic and anaerobic, to grow a mixture of microbes from the sampled sediment. The strains grown were then isolated on Zobell marine agar or solidified artificial seawater medium until pure, then phenotypically characterized using a MicroArray analysis. This method enumerated a variety of hydrocarbon degrading microorganisms, the majority of which were gammaproteobacteria. The most prevalent of these was Alcanivorax spp., which were shown to have the highest MPN (most probable number) counts and were seen to be more frequently found in visibly oil-contaminated sand samples. As oil is a major carbon source, the overall number of microbes increased with more contaminated samples as there was more energy readily available for them to utilize. This is good news in terms of oil spill clean-up in this area, as it means indigenous microbial communities are capable of reacting quickly and efficiently to spills. Maximum abundance was shown to be at 1-2 weeks after the contamination, this proves that a natural clean-up may be the best option for the recovery of this environment.

  Of the 24 hydrocarbon degrading bacteria isolated the most effect at this site appeared to be closely related to Alanivorax dieslolei, with 93% oil degradation, followed by what was thought to be Acinetobacter sp. at 90%. These bacteria seemed to be thriving rather than surviving on the oil contamination therefore, when oil contamination was reduced, A. dieslolei counts did also fell in number. It appeared to be less versatile than the other gammaproteobacteria sampled.

The second method of microbe enumeration involved molecular techniques. DNA and RNA were extracted using the automated ribosomal intragenic spacer analysis (ARISA) method and GoScript reverse transcriptase. These extracted samples were then sequenced using one-step PCR and analysed in QIIME and Primer6 software to build a phylogenetic tree. This technique allowed for a larger sample size and a quicker comparison of species. It showed that contrary to the known culturability of bacteria, similar numbers of oil degrading bacteria were found from both culturing and molecular techniques. This shows potential for commercial applications of these bacteria as they can be easily cultured in the lab and could be used as a solution in areas of oil spill as an artificially induced bioremediation defence. The microbe that showed the most potential of commercial use was Alanivorax dieslolei.

The Alanivorax genus was selected for specifically with these molecular techniques and the use of a probe labelled with fluorescent dye to allow for quantification of this already known to be hydrocarbon degrading genus. The species though to be Alanivorax dieslolei had the highest consumption rate and only thrives in areas of high oil concentration, meaning it could potentially aid with the cleaning up of oil spills without too much interference on natural populations. This is because it will only thrive until the oil is depleted, at which point indigenous microbial communities can return to normal function.

My personal opinion is that this paper is only a first glance into community structure of oil spill clean ups. New techniques such as metagenomics could provide a more substantial overview of the populations involved at different stages of a clean-up. I believe that this paper is a step in the right direction as understanding the way in which the environment will recover from these events naturally will enable us to find the best possible way to deal with them in the future.

Kostka, J. E., Prakash, O., Overholt, W.A., Green, S. J., Freyer, G., Canion, A., Delgardio, J., Norton, N., Hazen T.C. and Huettel M. (2011) Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill. Applied Environmental Microbiology 77, 22, 7963-7974.